New insights into FeS/persulfate system for tetracycline elimination: Iron valence, homogeneous-heterogeneous reactions and degradation pathways.

In this study, complete tetracycline (TTC) and above 50% of total organic carbon (TOC) were removed by FeS/PS after 30 min under optimized conditions. Although free radicals and high-valent iron ions were identified to generate in the process, the apparent similarity between intermediate products of FeS/PS, Fe/PS, and UV/PS systems demonstrated that the degradation of TTC was due to sulfate radicals (SO4⋅-) and hydroxyl radicals (⋅OH). Based on the reaction between free radicals and organic matter, we speculated that TTC in the FeS/PS system was decomposed and mineralized by dehydration, dehydrogenation, hydroxyl addition, demethylation, substitution, E-transfer, and ring-opening. Furthermore, a new understanding of FeS-mediated PS activation based on stoichiometry and kinetic analysis showed that there were both homogeneous and heterogeneous reactions that occurred in the entire progress. However, due to the effect of pH on the dissolution of iron ions, the homogeneous reaction became the principal process with iron ions concentration exceeding 1.35 mg/L. This work provides a theoretical basis for the study of the degradation of TTC-containing wastewater by the iron-based advanced oxidation process.

Residue measurement of pendimethalin in tobacco by using heart-cutting two dimensional liquid chromatography coupled with tandem mass spectrometry.

A novel heart-cutting two-dimensional liquid chromatography coupled with tandem mass spectrometry method was developed for quantitative analysis of pendimethalin residue in tobacco. The strategy of reversed phase liquid chromatography coupled with another reversed-phase liquid chromatography was employed for high column efficiency and excellent compatibility of mobile phase. In the first dimensional chromatography, a cyano column with methanol/water as the eluent was applied to separate pendimethalin from thousands of interference components in tobacco. By heart-cutting technique, which effectively removed interference components, the target compound was cut to the second dimensional C18 column for further separation. The pendimethalin residue was finally determined by the tandem mass spectrometry under multiple reaction monitoring reversed-phase liquid chromatography mode. Sample pretreatment of the new method was simplified, involving only extraction and filtration. Compared with traditional methodologies, the new method showed fairly high selectivity and sensitivity with almost no matrix interference. The limit of quantitation for pendimethalin was 1.21 ng/mL, whereas the overall recoveries ranged from 95.7 to 103.3%. The new method has been successfully applied to non-stop measure of 200 real samples, without contamination of ion source. Detection results of the samples agreed well with standard method.

Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease.

Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansion in the gene-encoding Huntingtin (HTT). Transcriptome dysregulation is a major feature of HD pathogenesis, as revealed by a large body of work on gene expression profiling of tissues from human HD patients and mouse models. These studies were primarily focused on transcriptional changes affecting steady-state overall gene expression levels using microarray based approaches. A major missing component, however, has been the study of transcriptome changes at the post-transcriptional level, such as alternative splicing. Alternative splicing is a critical mechanism for expanding regulatory and functional diversity from a limited number of genes, and is particularly complex in the mammalian brain. Here we carried out a deep RNA-seq analysis of the BA4 (Brodmann area 4) motor cortex from seven human HD brains and seven controls to systematically discover aberrant alternative splicing events and characterize potential associated splicing factors in HD. We identified 593 differential alternative splicing events between HD and control brains. Using two expanded panels with a total of 108 BA4 tissues from patients and controls, we identified four splicing factors exhibiting significantly altered expression levels in HD patient brains. Moreover, follow-up molecular analyses of one splicing factor PTBP1 revealed its impact on disease-associated splicing patterns in HD. Collectively, our data provide genomic evidence for widespread splicing dysregulation in HD brains, and suggest the role of aberrant alternative splicing in the pathogenesis of HD.

rMATS-DVR: rMATS discovery of differential variants in RNA.

MOTIVATION: RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a specific perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular states. Such differential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA processing, as well as changes in RNA editing in response to cellular perturbations or stimuli. RESULTS: We have developed rMATS-DVR, a convenient and user-friendly software program to streamline the discovery of DVRs between two RNA-seq sample groups with replicates. rMATS-DVR combines a stringent GATK-based pipeline for calling SNVs including SNPs and RNA editing events in RNA-seq reads, with our rigorous rMATS statistical model for identifying differential isoform ratios using RNA-seq sequence count data with replicates. We applied rMATS-DVR to RNA-seq data of the human chronic myeloid leukemia cell line K562 in response to shRNA knockdown of the RNA editing enzyme ADAR1. rMATS-DVR discovered 1372 significant DVRs between knockdown and control. These DVRs encompassed known SNPs and RNA editing sites as well as novel SNVs, with the majority of DVRs corresponding to known RNA editing sites repressed after ADAR1 knockdown. AVAILABILITY AND IMPLEMENTATION: rMATS-DVR is at https://github.com/Xinglab/rMATS-DVR . CONTACT: yxing@ucla.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data.

Ultra-deep RNA sequencing (RNA-Seq) has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We previously developed multivariate analysis of transcript splicing (MATS), a statistical method for detecting differential alternative splicing between two RNA-Seq samples. Here we describe a new statistical model and computer program, replicate MATS (rMATS), designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates. In addition to the analysis of unpaired replicates, rMATS also includes a model specifically designed for paired replicates between sample groups. The hypothesis-testing framework of rMATS is flexible and can assess the statistical significance over any user-defined magnitude of splicing change. The performance of rMATS is evaluated by the analysis of simulated and real RNA-Seq data. rMATS outperformed two existing methods for replicate RNA-Seq data in all simulation settings, and RT-PCR yielded a high validation rate (94%) in an RNA-Seq dataset of prostate cancer cell lines. Our data also provide guiding principles for designing RNA-Seq studies of alternative splicing. We demonstrate that it is essential to incorporate biological replicates in the study design. Of note, pooling RNAs or merging RNA-Seq data from multiple replicates is not an effective approach to account for variability, and the result is particularly sensitive to outliers. The rMATS source code is freely available at rnaseq-mats.sourceforge.net/. As the popularity of RNA-Seq continues to grow, we expect rMATS will be useful for studies of alternative splicing in diverse RNA-Seq projects.

Similarity of markers identified from cancer gene expression studies: observations from GEO.

Gene expression profiling has been extensively conducted in cancer research. The analysis of multiple independent cancer gene expression datasets may provide additional information and complement single-dataset analysis. In this study, we conduct multi-dataset analysis and are interested in evaluating the similarity of cancer-associated genes identified from different datasets. The first objective of this study is to briefly review some statistical methods that can be used for such evaluation. Both marginal analysis and joint analysis methods are reviewed. The second objective is to apply those methods to 26 Gene Expression Omnibus (GEO) datasets on five types of cancers. Our analysis suggests that for the same cancer, the marker identification results may vary significantly across datasets, and different datasets share few common genes. In addition, datasets on different cancers share few common genes. The shared genetic basis of datasets on the same or different cancers, which has been suggested in the literature, is not observed in the analysis of GEO data.

Low-Intensity Pulsed Ultrasound Treatment at an Early Osteoarthritis Stage Protects Rabbit Cartilage From Damage via the Integrin/Focal Adhesion Kinase/Mitogen-Activated Protein Kinase Signaling Pathway.

OBJECTIVES: To investigate whether low-intensity pulsed ultrasound (US) has different protective effects on early and late rabbit osteoarthritis cartilage via the integrin/focal adhesion kinase (FAK)/mitogen-activated protein kinase (MAPK) signaling pathway. METHODS: Thirty-six New Zealand White rabbits were divided into early control, early osteoarthritis, early treatment, late control, late osteoarthritis, and late treatment groups. The early and late osteoarthritis and treatment groups underwent anterior cruciate ligament transection. The remaining groups underwent sham operations with knee joint exposure. The early and late treatment groups were exposed to low-intensity pulsed US 4 and 8 weeks after surgery. After 6 weeks of US exposure, pathologic changes on the articular surface of the femoral condyle were assessed by modified Mankin scores. Expression of type II collagen, matrix metalloproteinase, integrin ß1, phosphorylated FAK, and MAPKs (including extracellular signal-regulated kinase 1/2, MAPK 38, and c-Jun N-terminal kinase) was assessed by Western blot analysis. RESULTS: Cartilage damage was less severe in the early treatment group than the early osteoarthritis group. The Mankin score was significantly lower in the early treatment group than the early osteoarthritis group (P < .05). There was no significant difference in cartilage damage or Mankin score between the late treatment and late osteoarthritis groups. There was a significant increase in type II collagen expression but a significant decrease in matrix metalloproteinase 13 expression in the early treatment group compared to the early osteoarthritis group, whereas no significant difference was found between the late treatment and late osteoarthritis groups. Integrin ß1 and phosphorylated FAK expression was significantly higher, and phosphorylated extracellular signal-regulated kinase 1/2 and phosphorylated MAPK 38 expression was significantly lower in the early treatment group than the early osteoarthritis group. CONCLUSIONS: Our findings indicate that low-intensity pulsed US protects cartilage from damage in early-stage osteoarthritis via the integrin/FAK/MAPK pathway.

An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition.

Alternative splicing achieves coordinated changes in post-transcriptional gene expression programmes through the activities of diverse RNA-binding proteins. Epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) are cell-type-specific regulators of transcripts that switch splicing during the epithelial-mesenchymal transition (EMT). To define a comprehensive programme of alternative splicing that is regulated during the EMT, we identified an extensive ESRP-regulated splicing network of hundreds of alternative splicing events within numerous genes with functions in cell-cell adhesion, polarity, and migration. Loss of this global ESRP-regulated epithelial splicing programme induces the phenotypic changes in cell morphology that are observed during the EMT. Components of this splicing signature provide novel molecular markers that can be used to characterize the EMT. Bioinformatics and experimental approaches revealed a high-affinity ESRP-binding motif and a predictive RNA map that governs their activity. This work establishes the ESRPs as coordinators of a complex alternative splicing network that adds an important post-transcriptional layer to the changes in gene expression that underlie epithelial-mesenchymal transitions during development and disease.

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.

Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (multivariate analysis of transcript splicing), a bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data. MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P-value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern. We evaluated the performance of MATS using simulated and real RNA-Seq data sets. In the RNA-Seq analysis of alternative splicing events regulated by the epithelial-specific splicing factor ESRP1, we obtained a high RT-PCR validation rate of 86% for differential exon skipping events with a MATS FDR of <10%. Additionally, over the full list of RT-PCR tested exons, the MATS FDR estimates matched well with the experimental validation rate. Our results demonstrate that MATS is an effective and flexible approach for detecting differential alternative splicing from RNA-Seq data.

Widespread establishment and regulatory impact of Alu exons in human genes.

The Alu element has been a major source of new exons during primate evolution. Thousands of human genes contain spliced exons derived from Alu elements. However, identifying Alu exons that have acquired genuine biological functions remains a major challenge. We investigated the creation and establishment of Alu exons in human genes, using transcriptome profiles of human tissues generated by high-throughput RNA sequencing (RNA-Seq) combined with extensive RT-PCR analysis. More than 25% of Alu exons analyzed by RNA-Seq have estimated transcript inclusion levels of at least 50% in the human cerebellum, indicating widespread establishment of Alu exons in human genes. Genes encoding zinc finger transcription factors have significantly higher levels of Alu exonization. Importantly, Alu exons with high splicing activities are strongly enriched in the 5'-UTR, and two-thirds (10/15) of 5'-UTR Alu exons tested by luciferase reporter assays significantly alter mRNA translational efficiency. Mutational analysis reveals the specific molecular mechanisms by which newly created 5'-UTR Alu exons modulate translational efficiency, such as the creation or elongation of upstream ORFs that repress the translation of the primary ORFs. This study presents genomic evidence that a major functional consequence of Alu exonization is the lineage-specific evolution of translational regulation. Moreover, the preferential creation and establishment of Alu exons in zinc finger genes suggest that Alu exonization may have globally affected the evolution of primate and human transcriptomes by regulating the protein production of master transcriptional regulators in specific lineages.

Evolution of alternative splicing in primate brain transcriptomes.

Alternative splicing is a predominant form of gene regulation in higher eukaryotes. The evolution of alternative splicing provides an important mechanism for the acquisition of novel gene functions. In this work, we carried out a genome-wide phylogenetic survey of lineage-specific splicing patterns in the primate brain, via high-density exon junction array profiling of brain transcriptomes of humans, chimpanzees and rhesus macaques. We identified 509 genes showing splicing differences among these species. RT-PCR analysis of 40 exons confirmed the predicted splicing evolution of 33 exons. Of these 33 exons, outgroup analysis using rhesus macaques confirmed 13 exons with human-specific increase or decrease in transcript inclusion levels after humans diverged from chimpanzees. Some of the human-specific brain splicing patterns disrupt domains critical for protein-protein interactions, and some modulate translational efficiency of their host genes. Strikingly, for exons showing splicing differences across species, we observed a significant increase in the rate of silent substitutions within exons, coupled with accelerated sequence divergence in flanking introns. This indicates that evolution of cis-regulatory signals is a major contributor to the emergence of human-specific splicing patterns. In one gene (MAGOH), using minigene reporter assays, we demonstrated that the combination of two human-specific cis-sequence changes created its human-specific splicing pattern. Together, our data reveal widespread human-specific changes of alternative splicing in the brain and suggest an important role of splicing in the evolution of neuronal gene regulation and functions.

The nuclear experience of CPEB: implications for RNA processing and translational control.

CPEB is a sequence-specific RNA binding protein that promotes polyadenylation-induced translation in early development, during cell cycle progression and cellular senescence, and following neuronal synapse stimulation. It controls polyadenylation and translation through other interacting molecules, most notably the poly(A) polymerase Gld2, the deadenylating enzyme PARN, and the eIF4E-binding protein Maskin. Here, we report that CPEB shuttles between the nucleus and cytoplasm and that its export occurs via the CRM1-dependent pathway. In the nucleus of Xenopus oocytes, CPEB associates with lampbrush chromosomes and several proteins involved in nuclear RNA processing. CPEB also interacts with Maskin in the nucleus as well as with CPE-containing mRNAs. Although the CPE does not regulate mRNA export, it influences the degree to which mRNAs are translationally repressed in the cytoplasm. Moreover, CPEB directly or indirectly mediates the alternative splicing of at least one pre-mRNA in mouse embryo fibroblasts as well as certain mouse tissues. We propose that CPEB, together with Maskin, binds mRNA in the nucleus to ensure tight translational repression upon export to the cytoplasm. In addition, we propose that nuclear CPEB regulates specific pre-mRNA alternative splicing.

Challenges, opportunities, and innovative statistical designs for precision oncology trials.

In the era of precision oncology, improved understanding of tumor heterogeneity, particularly at the molecular level, has caused a shift from traditionally histology based cancer drug development to molecularly targeted drug development. The shift to the molecular view of cancer leads to increasingly small cancer populations for clinical trials which may be underpowered using traditional statistical designs. This paradigm shift lead to the recent developments of innovative clinical trial designs to address the challenges from precision oncology clinical trials. Hence, this paper reviewed and described innovative trial designs for precision oncology. Different strategies were discussed to account patient and treatment effect heterogeneity, including precision dose-finding designs that tailor the optimal dose to different patients at different time points, master protocol designs that match patients' molecular alterations with specific targeted agents, and adaptive enrichment designs that dynamically modify eligibility criteria and enroll patients that are most likely to benefit from the novel agents. Despite their superior performance, better understanding of practical barriers is needed to widen their implementation for precision oncology trials. Therefore, this paper also reviewed the practical challenges regarding the implementation of precision oncology clinical trials, along with the strength and weakness of various approaches of precision oncology clinical trial designs.

Enhanced degradation of tetracycline by Cu(II) complexation in the FeS/sulfite system.

This study applied a mineral material of FeS to activate sulfite for efficient degradation of TTC in the presence of Cu(II) based on the identified complexation mechanism through UV-Vis spectra, FTIR spectroscopy and DFT calculation. pH plays an important role in TTC degradation and the initial pH of 6 and 7 were the divide in the contributions of FeS/sulfite oxidation and complex-precipitation. TTC-Cu(II) exhibits a superior promoting effect on the TTC degradation in FeS/sulfite system due to the improvement of TTC electron transfer reactivity and Fe(II) dissolution from FeS. Moreover, the formation of Cu(I) improved the recycling of Fe(II) from Fe(III). Dissolved oxygen-dependent free radicals' generation was confirmed, and TTC degradation was mainly attributed to SO4·- and ·OH. The characterization of FeS surface through XPS, XRD, SEM-EDS, Fe(II) deactivation tests, together with the comparison of pseudo-first-order rate constants for TTC degradation by FeS and ferrous ion supported the important role of surface and dissolved Fe(II) in sulfite activation. Furthermore, reasonable degradation pathways of TTC have been proposed according to the detected products by LC-MS. This work highlights the important role of pH, DO and Cu(II) complexation in sulfite activation and TTC degradation, furnishing theoretical support for further relevant studies.

Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes.

Transposable elements (TEs) are major sources of new exons in higher eukaryotes. Almost half of the human genome is derived from TEs, and many types of TEs have the potential to exonize. In this work, we conducted a large-scale analysis of human exons derived from mammalian-wide interspersed repeats (MIRs), a class of old TEs which was active prior to the radiation of placental mammals. Using exon array data of 328 MIR-derived exons and RT-PCR analysis of 39 exons in 10 tissues, we identified 15 constitutively spliced MIR exons, and 15 MIR exons with tissue-specific shift in splicing patterns. Analysis of RNAs from multiple species suggests that the splicing events of many strongly included MIR exons have been established before the divergence of primates and rodents, while a small percentage result from recent exonization during primate evolution. Interestingly, exon array data suggest substantially higher splicing activities of MIR exons when compared with exons derived from Alu elements, a class of primate-specific retrotransposons. This appears to be a universal difference between exons derived from young and old TEs, as it is also observed when comparing Alu exons to exons derived from LINE1 and LINE2, two other groups of old TEs. Together, this study significantly expands current knowledge about exonization of TEs. Our data imply that with sufficient evolutionary time, numerous new exons could evolve beyond the evolutionary intermediate state and contribute functional novelties to modern mammalian genomes.

MADS+: discovery of differential splicing events from Affymetrix exon junction array data.

MOTIVATION: The Affymetrix Human Exon Junction Array is a newly designed high-density exon-sensitive microarray for global analysis of alternative splicing. Contrary to the Affymetrix exon 1.0 array, which only contains four probes per exon and no probes for exon-exon junctions, this new junction array averages eight probes per probeset targeting all exons and exon-exon junctions observed in the human mRNA/EST transcripts, representing a significant increase in the probe density for alternative splicing events. Here, we present MADS+, a computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events. For example, in a study of the novel epithelial-specific splicing regulator ESRP1, MADS+ detects hundreds of exons whose inclusion levels are dependent on ESRP1, with a RT-PCR validation rate of 88.5% (153 validated out of 173 tested). AVAILABILITY: MADS+ scripts, documentations and annotation files are available at http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/.

Diverse splicing patterns of exonized Alu elements in human tissues.

Exonization of Alu elements is a major mechanism for birth of new exons in primate genomes. Prior analyses of expressed sequence tags show that almost all Alu-derived exons are alternatively spliced, and the vast majority of these exons have low transcript inclusion levels. In this work, we provide genomic and experimental evidence for diverse splicing patterns of exonized Alu elements in human tissues. Using Exon array data of 330 Alu-derived exons in 11 human tissues and detailed RT-PCR analyses of 38 exons, we show that some Alu-derived exons are constitutively spliced in a broad range of human tissues, and some display strong tissue-specific switch in their transcript inclusion levels. Most of such exons are derived from ancient Alu elements in the genome. In SEPN1, mutations of which are linked to a form of congenital muscular dystrophy, the muscle-specific inclusion of an Alu-derived exon may be important for regulating SEPN1 activity in muscle. Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity after the divergence of humans and chimpanzees. Our results imply that some Alu exonization events may have acquired adaptive benefits during the evolution of primate transcriptomes.

phase1RMD: An R package for repeated measures dose-finding designs with novel toxicity and efficacy endpoints.

Traditional dose-finding designs are substantially inefficient for targeted agents and cancer immunotherapies by failing to incorporate efficacy signals, mild and moderate adverse events, and late, cumulative toxicities. However, the lack of user-friendly software is a barrier to the practical use of the novel phase I designs, despite their demonstrated superiority of traditional 3+3 designs. To overcome these barriers, we present an R package, phase1RMD, which provides a comprehensive implementation of novel designs with repeated toxicity measures and early efficacy. A novel phase I repeated measures design that used a continuous toxicity score from multiple treatment cycles was implemented. Furthermore, in studies where preliminary efficacy is evaluated, an adaptive, multi-stage design to identify the most efficacious dose with acceptable toxicity was demonstrated. Functions are provided to recommend the next dose based on the data collected in a phase I trial, as well as to assess trial characteristics given design parameters via simulations. The repeated measure designs accurately estimated both the magnitude and direction of toxicity trends in late treatment cycles, and allocated more patients at therapeutic doses. The R package for implementing these designs is available from the Comprehensive R Archive Network. To our best knowledge, this is the first software that implement novel phase I dose-finding designs that simultaneously accounts for the multiple-grade toxicity events over multiple treatment cycles and a continuous early efficacy outcome. With the software published on CRAN, we will pursue the implementation of these designs in phase I trials in real-life settings.

MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays.

We describe a method, microarray analysis of differential splicing (MADS), for discovery of differential alternative splicing from exon-tiling microarray data. MADS incorporates a series of low-level analysis algorithms motivated by the "probe-rich" design of exon arrays, including background correction, iterative probe selection, and removal of sequence-specific cross-hybridization to off-target transcripts. We used MADS to analyze Affymetrix Exon 1.0 array data on a mouse neuroblastoma cell line after shRNA-mediated knockdown of the splicing factor polypyrimidine tract binding protein (PTB). From a list of exons with predetermined inclusion/exclusion profiles in response to PTB depletion, MADS recognized all exons known to have large changes in transcript inclusion levels and offered improvement over Affymetrix's analysis procedure. We also identified numerous novel PTB-dependent splicing events. Thirty novel events were tested by RT-PCR and 27 were confirmed. This work demonstrates that the exon-tiling microarray design is an efficient and powerful approach for global, unbiased analysis of pre-mRNA splicing.

Nonallele-specific silencing of mutant and wild-type huntingtin demonstrates therapeutic efficacy in Huntington's disease mice.

Huntington's disease (HD) is a fatal neurodegenerative disease caused by mutant huntingtin (htt) protein, and there are currently no effective treatments. Recently, we and others demonstrated that silencing mutant htt via RNA interference (RNAi) provides therapeutic benefit in HD mice. We have since found that silencing wild-type htt in adult mouse striatum is tolerated for at least 4 months. However, given the role of htt in various cellular processes, it remains unknown whether nonallele-specific silencing of both wild-type and mutant htt is a viable therapeutic strategy for HD. Here, we tested whether cosilencing wild-type and mutant htt provides therapeutic benefit and is tolerable in HD mice. After treatment, HD mice showed significant reductions in wild-type and mutant htt, and demonstrated improved motor coordination and survival. We performed transcriptional profiling to evaluate the effects of reducing wild-type htt in adult mouse striatum. We identified gene expression changes that are concordant with previously described roles for htt in various cellular processes. Also, several abnormally expressed transcripts associated with early-stage HD were differentially expressed in our studies, but intriguingly, those involved in neuronal function changed in opposing directions. Together, these encouraging and surprising findings support further testing of nonallele-specific RNAi therapeutics for HD.